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- EMDB-80402: side fiber of F2-pyocin -

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Basic information

Entry
Database: EMDB / ID: EMD-80402
Titleside fiber of F2-pyocin
Map data
Sample
  • Complex: F2-pyocin Cap
    • Protein or peptide: F2-pyocin side fiber
Keywordspyocin / phage / cap / VIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsGu ZW / Xie YF / Wang JW
Funding support China, 1 items
OrganizationGrant numberCountry
Other government5262009 China
CitationJournal: Adv Sci (Weinh) / Year: 2026
Title: F-Type Pyocin Versus Phage λ Tail: Conserved Hub, Divergent Fibers.
Authors: Zhiwei Gu / Yufan Xie / Lanxin Wang / Luyan Ma / Xiaofei Ge / Jiawei Wang /
Abstract: Bacteriocins are ribosomally synthesized antimicrobial peptides or proteins that offer an alternative to conventional antibiotics against multidrug-resistant pathogens. Phage tail-like bacteriocins ...Bacteriocins are ribosomally synthesized antimicrobial peptides or proteins that offer an alternative to conventional antibiotics against multidrug-resistant pathogens. Phage tail-like bacteriocins (tailocins) are classified into rigid R-type and flexible F-type variants. While R-type pyocins from Pseudomonas aeruginosa are well-characterized, F-type pyocins remain poorly understood, especially with respect to the molecular mechanisms for their Gram-negative bactericidal activity. Here, we report cryo-electron microscopy structures of the F-type pyocin from P. aeruginosa ATCC 15442 at 2.29-3.26 Å resolution, encompassing three modular components: the tail cap, tail tip, and tail fiber. Structural comparisons with bacteriophage λ reveal a conserved tail tip architecture, including the baseplate hub proteins, distal tail protein, tail assembly protein, and tape measure protein. Unexpectedly, we identify three trimeric side fibers that attach not to the distal tail protein, as in canonical systems, but to the α-helical shaft of the central fiber, indicating a previously unrecognized attachment mode. The receptor-binding domain of the side fiber shares structural similarity with LPS-recognizing domains of R-type pyocins. Together, these results define the structural basis of F-type pyocin assembly and host recognition, reveal conserved and unique features relative to phage λ, and provide a framework for engineering tailocins as precision antimicrobials against drug-resistant P. aeruginosa.
History
DepositionApr 19, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80402.png

Downloads & links

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Map

FileDownload / File: emd_80402.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 237.056 Å		0.93 Å/pix.
x 256 pix.
= 237.056 Å		0.93 Å/pix.
x 256 pix.
= 237.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.688
Minimum - Maximum-2.921621 - 4.631546
Average (Standard dev.)0.000664367 (±0.11780166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 237.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80402_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80402_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : F2-pyocin Cap

EntireName: F2-pyocin Cap
Components
  • Complex: F2-pyocin Cap
    • Protein or peptide: F2-pyocin side fiber

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Supramolecule #1: F2-pyocin Cap

SupramoleculeName: F2-pyocin Cap / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: F2-pyocin side fiber

MacromoleculeName: F2-pyocin side fiber / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 38.697773 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: MAWHSKGSVS VTLNSEAVLG NATDFIANVR TGDAFRGPDG RWYEITNVTS ATVISIKPNY QGATASGQVY AVVPIHGYSK NLADQFRDI NNQWGATLAG IKPWAVSSTG QQAQADMGIS AVGRALNNAS TPANALSYLG GVAPNQMGWA GNAMNTADLD S LTVSGLYA ...String:
MAWHSKGSVS VTLNSEAVLG NATDFIANVR TGDAFRGPDG RWYEITNVTS ATVISIKPNY QGATASGQVY AVVPIHGYSK NLADQFRDI NNQWGATLAG IKPWAVSSTG QQAQADMGIS AVGRALNNAS TPANALSYLG GVAPNQMGWA GNAMNTADLD S LTVSGLYA HGTAVPSPVN NAQGYVLHMQ HGNPDFAVQQ WYQLNSATGQ YMRIKAGGNW SRWVLQYSQF NLVGLASFDA SN NPSGAII QRGGTVGFNE YVRYADGTQI CWGNTTTNVG ATMAYQPAGT LSFYITPVAY SWGFPVSFSR PPSVMVNPMR AAG NNASRP WGSTMSVTET LFSWYGYDTA SVASGMAASY VAMGRWN

UniProtKB: UNIPROTKB: A0A2V3GUQ2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.91 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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